AMBER Archive (2009)

Subject: Re: [AMBER] problem in rmsd

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Mar 09 2009 - 22:25:18 CDT

> I am facing a weird problem while calculating the rmsd using
> ptraj. I am doing the canonical simulation of TrpCage miniprotein at
> 325k. I followed the steps available online (provided by ross
> Walker ). After heating the system to the desired temperature, I
> created a pdb file and it looks reasonable. Then I performed 100ps
> short canonical MD at this temperature and stored the configuration
> in every 50 steps (ntwx=50). While I calculated the rmsd of the
> trajectory from the experimental nmr structure, I found that 3rd &
> 4th snapshots give absurd rmsd (300+ AA). If I make ntwx=1, still I
> found that 3rd & 4th snapshots gives absurd rmsd.

300+ Angstrom is indeed absurb. What I would do is output PDB files for
each frame and look at them. Make sure there is not a mismatch in the
prmtop/mdcrd; look at the energies over the simulation... --tec3

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